Started by upstream project "BIOFORMATS-test-repo" build number 281
originally caused by:
Started by upstream project "Trigger" build number 301
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4
[BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins4508879832054231122.sh
+ '[' samples = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_44303_merge_ci -v /uod/idr/repos/curated/samples:/data -v /uod/idr-scratch/merge-ci/curated/samples:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12
Buildfile: /bio-formats-build/bioformats/components/test-suite/build.xml
[echo] isSnapshot = true
init-title:
[echo] ----------=========== bio-formats-testing-framework ===========----------
init-timestamp:
init:
copy-resources:
compile:
[resolver:resolve] Resolving artifacts
compile-tests:
[resolver:resolve] Resolving artifacts
[javac] Compiling 1 source file to /bio-formats-build/bioformats/components/test-suite/test
test-automated:
[testng] File leak detector installed
[testng] 00:36:00,529 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 00:36:00,530 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service.
[testng] 00:36:00,530 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:36:00,531 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:36:00,531 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 00:36:00,532 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 00:36:00,532 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 00:36:00,532 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:36:00,532 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:36:00,533 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 00:36:00,533 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 00:36:00,533 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 00:36:00,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 00:36:00,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 00:36:00,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 00:36:00,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 00:36:00,789 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 00:36:00,789 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 00:36:00,789 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 00:36:00,790 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 00:36:00,790 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration.
[testng] 00:36:00,790 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point
[testng] 00:36:00,791 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 259 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-12-06 00:36:00,800] [main] java.version = 1.8.0_342
[testng] 00:36:00,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 00:36:00,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:36:00,863 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-06_00-36-00.log]
[testng] 00:36:00,865 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration.
[testng] [2024-12-06 00:36:00,868] [main] testng.directory = /data
[testng] [2024-12-06 00:36:00,868] [main] testng.configDirectory = /config
[testng] [2024-12-06 00:36:00,887] [main] testng.multiplier = 1.0
[testng] [2024-12-06 00:36:00,887] [main] testng.in-memory = false
[testng] [2024-12-06 00:36:00,887] [main] testng.allow-missing = false
[testng] [2024-12-06 00:36:00,887] [main] user.language = en
[testng] [2024-12-06 00:36:00,887] [main] user.country = ${user.country}
[testng] [2024-12-06 00:36:00,888] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-12-06 00:36:31,050] [main] ----------------------------------------
[testng] [2024-12-06 00:36:31,050] [main] Total files: 164
[testng] [2024-12-06 00:36:31,051] [main] Scan time: 30.162 s (183 ms/file)
[testng] [2024-12-06 00:36:31,051] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 59 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-12-06 00:37:45,010] [pool-1-thread-1] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK:
[testng] 00:37:45,011 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 00:37:45,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:45,014 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-06_00-37-45.log]
[testng] 00:37:45,016 |-INFO in ch.qos.logback.core.sift.SiftProcessor@602a8caf - End of configuration.
[testng] [2024-12-06 00:37:46,350] [pool-1-thread-12] Initializing /data/openjpeg/FacadeERROPJW.bmp:
[testng] 00:37:46,350 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 00:37:46,350 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:46,351 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-06_00-37-46.log]
[testng] 00:37:46,351 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e6d141a - End of configuration.
[testng] [2024-12-06 00:37:46,539] [pool-1-thread-11] Initializing /data/ome/t0_pos1-0_5x.lsm:
[testng] 00:37:46,540 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 00:37:46,540 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:46,540 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-06_00-37-46.log]
[testng] 00:37:46,541 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52c085b1 - End of configuration.
[testng] [2024-12-06 00:37:47,394] [pool-1-thread-10] Initializing /data/ome/Adultmidsection.lsm:
[testng] 00:37:47,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 00:37:47,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:47,395 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-06_00-37-47.log]
[testng] 00:37:47,395 |-INFO in ch.qos.logback.core.sift.SiftProcessor@97dae36 - End of configuration.
[testng] [2024-12-06 00:37:48,174] [pool-1-thread-9] Initializing /data/ome/654Atemp.stk:
[testng] 00:37:48,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 00:37:48,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:48,175 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-06_00-37-48.log]
[testng] 00:37:48,175 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d46184e - End of configuration.
[testng] [2024-12-06 00:37:50,697] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.bmp:
[testng] 00:37:50,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 00:37:50,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:50,698 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-06_00-37-50.log]
[testng] 00:37:50,699 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5790e2a5 - End of configuration.
[testng] [2024-12-06 00:37:50,791] [pool-1-thread-7] Initializing /data/ome/embryo.lsm:
[testng] 00:37:50,792 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 00:37:50,792 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:50,792 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-06_00-37-50.log]
[testng] 00:37:50,793 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bf506d1 - End of configuration.
[testng] [2024-12-06 00:37:51,412] [pool-1-thread-6] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg:
[testng] 00:37:51,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 00:37:51,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:51,413 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-06_00-37-51.log]
[testng] 00:37:51,413 |-INFO in ch.qos.logback.core.sift.SiftProcessor@122c6b61 - End of configuration.
[testng] [2024-12-06 00:37:51,540] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm:
[testng] 00:37:51,541 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 00:37:51,541 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:51,542 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-06_00-37-51.log]
[testng] 00:37:51,542 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a45989e - End of configuration.
[testng] [2024-12-06 00:37:51,945] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm:
[testng] 00:37:51,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 00:37:51,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:51,946 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-06_00-37-51.log]
[testng] 00:37:51,946 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22e730c9 - End of configuration.
[testng] [2024-12-06 00:37:51,994] [pool-1-thread-3] Initializing /data/ome/worm.tiff:
[testng] 00:37:51,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 00:37:51,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:51,994 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-06_00-37-51.log]
[testng] 00:37:51,995 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a987c78 - End of configuration.
[testng] [2024-12-06 00:37:52,886] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF:
[testng] 00:37:52,886 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 00:37:52,886 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:37:52,887 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-06_00-37-52.log]
[testng] 00:37:52,887 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1952b94f - End of configuration.
[testng] [2024-12-06 00:37:56,635] [pool-1-thread-4] Initializing /data/ome/C1.lsm:
[testng] [2024-12-06 00:37:57,065] [pool-1-thread-6] Initializing /data/openjpeg/Facade.bmp:
[testng] [2024-12-06 00:37:57,295] [pool-1-thread-8] Initializing /data/openjpeg/Rome.ppm:
[testng] [2024-12-06 00:37:57,432] [pool-1-thread-12] Initializing /data/ome/arwen0205_raw00201.pic:
[testng] [2024-12-06 00:37:58,770] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Bretagne2.jpg:
[testng] [2024-12-06 00:37:59,670] [pool-1-thread-7] Initializing /data/ome/anusgfpzs.lsm:
[testng] [2024-12-06 00:38:01,421] [pool-1-thread-10] Initializing /data/sdub/sdub.pattern:
[testng] [2024-12-06 00:38:07,200] [pool-1-thread-11] Initializing /data/ome/C1midmusnorm.lsm:
[testng] [2024-12-06 00:38:07,773] [pool-1-thread-8] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk:
[testng] [2024-12-06 00:38:08,700] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.bmp:
[testng] [2024-12-06 00:38:08,830] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.jp2:
[testng] [2024-12-06 00:38:10,374] [pool-1-thread-3] Initializing /data/openjpeg/Facade.pnm:
[testng] [2024-12-06 00:38:10,552] [pool-1-thread-6] Initializing /data/openjpeg/Rome.bmp:
[testng] [2024-12-06 00:38:11,047] [pool-1-thread-5] Initializing /data/ome/tiffany.color.tiff:
[testng] [2024-12-06 00:38:12,600] [pool-1-thread-4] Initializing /data/ome/cb_1.r3d:
[testng] [2024-12-06 00:38:12,907] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne1.j2k:
[testng] [2024-12-06 00:38:13,519] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.ppm:
[testng] [2024-12-06 00:38:13,841] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF:
[testng] [2024-12-06 00:38:15,114] [pool-1-thread-6] Initializing /data/ome/compressed2ChZ.lsm:
[testng] [2024-12-06 00:38:16,937] [pool-1-thread-3] Initializing /data/ome/tinyTest.d3d.dv:
[testng] [2024-12-06 00:38:17,212] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes2.ppm:
[testng] [2024-12-06 00:38:17,711] [pool-1-thread-4] Initializing /data/openjpeg/thumb_facade.jpg:
[testng] [2024-12-06 00:38:18,035] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne2.bmp:
[testng] [2024-12-06 00:38:18,255] [pool-1-thread-8] Initializing /data/mouse-kidney/mouse-kidney.lif:
[testng] [2024-12-06 00:38:19,407] [pool-1-thread-1] Initializing /data/ome/CHOBI_d3d.dv:
[testng] [2024-12-06 00:38:20,218] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.j2k:
[testng] [2024-12-06 00:38:20,680] [pool-1-thread-3] Initializing /data/ome/011B1_Morph.HTD:
[testng] [2024-12-06 00:38:22,361] [pool-1-thread-9] Initializing /data/ome/210502-0min-NFKB-4.r3d:
[testng] [2024-12-06 00:38:23,717] [pool-1-thread-7] Initializing /data/openjpeg/Rome.jp2:
[testng] [2024-12-06 00:38:24,223] [pool-1-thread-4] Initializing /data/ome/C1lowmusgfp.lsm:
[testng] [2024-12-06 00:38:25,672] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.bmp:
[testng] [2024-12-06 00:38:25,811] [pool-1-thread-5] Initializing /data/kidney_TFl/kidney_TFl.pattern:
[testng] [2024-12-06 00:38:26,870] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes1.jpg:
[testng] [2024-12-06 00:38:26,969] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Cevennes2.jpg:
[testng] [2024-12-06 00:38:27,332] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF:
[testng] [2024-12-06 00:38:30,303] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne1.ppm:
[testng] [2024-12-06 00:38:30,416] [pool-1-thread-1] Initializing /data/ome/n2_plate18_P24_w1.tif:
[testng] [2024-12-06 00:38:32,702] [pool-1-thread-12] Initializing /data/TAABA/TAABA.pattern:
[testng] [2024-12-06 00:38:59,397] [pool-1-thread-8] Initializing /data/ome/t1_pos1-0_5x.lsm:
[testng] [2024-12-06 00:39:00,051] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne2.j2k:
[testng] [2024-12-06 00:39:00,808] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Rome.jpg:
[testng] [2024-12-06 00:39:01,458] [pool-1-thread-9] Initializing /data/ome/Cpharynxzs1.lsm:
[testng] [2024-12-06 00:39:04,596] [pool-1-thread-7] Initializing /data/openjpeg/FacadeERROPJ.bmp:
[testng] [2024-12-06 00:39:05,086] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Bretagne1.jpg:
[testng] [2024-12-06 00:39:05,216] [pool-1-thread-2] Initializing /data/10-31 E1/10-31 E1.tif:
[testng] [2024-12-06 00:39:09,394] [pool-1-thread-8] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK:
[testng] [2024-12-06 00:39:10,919] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Speedway.jpg:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 3127, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 4 minutes 53 seconds
Finished: SUCCESS